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E-GEOD-68596 - Genome-wide maps of nuclear lamina interactions in single human cells (CEL-seq)

Status
Released on 24 September 2015, last updated on 25 September 2015
Organism
Homo sapiens
Samples (1)
Protocols (4)
Description
Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large Lamina Associated Domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of ~400 maps reveals a core architecture of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts are more sensitive to a change in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, single-cell gene expression and chromatin accessibility analysis shows that loci with consistent NL contacts are expressed at lower levels and are more consistently inaccessible than loci with lower contact frequencies. These results highlight fundamental principles of single cell chromatin organization. In this dataset, single-cell mRNA sequencing results from 96 single KBM7 cells have been deposited
Experiment type
RNA-seq of coding RNA 
Contacts
Siddharth Subhas Dey <s.dey@hubrecht.eu>, Alexander van Oudenaarden, Bas van Steensel, Jop Kind, Siddharth S Dey
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-68596.idf.txt
Sample and data relationshipE-GEOD-68596.sdrf.txt
Processed data (1)E-GEOD-68596.processed.1.zip
Additional data (1)E-GEOD-68596.additional.1.zip
Links